In the Shadows
by Whattheydonttellus
Summary: Applejack and rainbow dash, long time friends have fallen into a dangerous world of assassins and templars. Recruited and trained, the two fight for peace and the brotherhood.
1. Chapter 1

In the shadows  
By rivers ulmer

AN: for anypony that may be confused when they read this, yes, they are the "human forms" of each charicter, but they till have traits like wings and magic. This is the beauty of reading a story as opposed to watching a movie, you get to imagine what they look like building off the story description, you can picture it like a cartoon, drawing, real life, anime, whatever, the point is you get to do some imagining.

Part 1: Welcoming

Applejack woke up early one morning, earlier than normal. She didnt have to be in the fields til seven am, the clock now read five 'o six. She got her butterfly knife off nightstand, and went down to make breakfast. The feeling of flipping the knife open and closed felt like rubbing dry glue between your fingers. It felt so natural, so right.

She poured a bowl of Pony'os and grabbed a spoon. Despite getting only four hours of sleep that night, applejack was wide awake. Applejack finished her cerial and trotted happily outside. The sun had not yet risen, but the air was amazing, clear, sweet, and the perfect temperature. Applejack looked out at ponyville, not a soul in sight. It was so peacful, so quiet.

Applejack walked into the barn and climbed the ladder to the loft above. The ceiling was only about a meter above the hay loft's floor, so she had to duck down to get to the last hay stack. Applejack pushed some of the straw aside and opened the crate beneath. Her secret stache of hard apple cyder. She picked up a bottle and pryed off the seal with her knife and took a couple sips, then she put the cap back and put the cyder back in the case.

Applejack went back into her home and got the bacon out of the fridge and slice open the bag with her knife. She slapped it all onto a frying pan and turned on the stove. Applebloom was imediatly woken up by the sweet smell of cooking bacon. She ran down the stairs to claim her share of the meat.

"Hey lil sis." Applejack greeted her sister.  
"Hey, i ssssssmmmmmmeeeellllllllllll bacon!" Applebloom yelled.  
"Hush, mac is still alseep."  
"Sorry."

The two shared a plate of bacon, and walked out to the barn. Applejack was now twenty five, her arms were toned from cuttting apples down from the trees with a heavy machette. Her hair was a golden blonde, it had almost been sunbleached from working in the fields for so long. She always wore her stetson hat, work boots, and brown leather fingerless gloves.

Applebloom was now twenty one, she had been working in the orchard with her sister for almost six years. Her arms were strong, but not as strang as applejack's, she was smaller and could climb better, so she could cut down apples just as fast as her sister when she jumped off the roots sticking out of the ground to get in a tree. They competed to see who could chop down the most apples in a day, applejack almost always won.

Rainbow dash was flying over SAA looking for her best friend. She spotted applejack in the south fields cutting down apples. She swooped down almost crashing right into the farm girl. "Hey AJ, what's up?"

"Same as the last twelve times ya asked me, workin." Applejack said with a smile. Applejack always thought of rainbow dash as her hest friend, more than twilight, pinkie pie, rarity, or fluttershy. They spent a lot of free time together. They had a sleep over almost every weekend, tonight would be one of those sleep overs.

"When you get off for lunch, meet me over at the pancake house."

"All right, sounds good. Ill se ya 'round noon." Rainbow dash flew off back to town. Applejack kept chopping away until mid day, when she walked into town. She flipped out her knife and flipped it back shut, over and over, she loved that feeling.

When applejack arrived at the pancake house, she found rainbow dash sitting at a booth. "Aren't pancakes usualy fer breakfast dashy?"

"Yeah, but i know how much you love them, and thought, why not?" Their server came up to take their order.

"Hi rainbow, hey AJ." It was fluttershy.  
"Howdy flutters, whatchya doin here?"  
"Well, all the animals are in the woods, and uh..." The timid pink-haired girl leaned in close, "...mating." Flutyershy whispered, then stood back upright. "And since their gone, i needed a side job."

"Great, now we can come and see you all the time and get a meal!" Rainbow dash got excited.  
"Yeah, it'll be great, now speaking of a meal, what do you guys want to eat?" Fluttershy asked.  
"Blueberry pancake stack, and make them extra thick." Rainbow ordered, applejack right after her.  
"Double whipped cream pancakes and bacon, make sure they really load the whip cream on, ive been in the fields and im hungry."

Five minutes later, the pink-haired girl returned with their food. "Dig in girls." And they did, AJ and rainbow dash stuffed their faces with the fluffy goodness. They both finished and talked for a moment, then they left paid the check and left a large tip for fluttershy. The whole time applejack felt like she was being watched, but thought nothing of it. They walked out and said their goodbyes, and rainbow dash flew off. The feeling that somebody was watching her increased as applejack walked back to the farm.

Applejack thought she heard somebody behind her, she turned around only to find that nobody was there. She heard noises from an alley to her left, she looked between the buildings, but again, nobody was there. She walked a little faster, almost running. Sweet Apple Acres was in sight. Applejack had her hand on her knife, ready for anything. Then all of the sudden, a hand reached out and pulled her into an alley. Applejack whipped out her knife, but her captor had already grabbed it and held it against her. The hooded figure had his hand over her mouth, preventing her from calling for help. Applejack struggled, but to no avail as her attacker held her tight against the brick wall. Applejack stopped struggeling when she realized trying to break free was a lost cause.

"I'm not going to hurt you, i just want to talk to you." The hooded man said, only his voice didnt sound very old, applejack guessed he couldnt be much older than herself. Two more figures accompanied the boy, another boy with a black coat that had navy blue trimmings, and a girl, an ash grey coat with white trimmings, her face was covered but a lock if rainbow colored hair flowed down her left shoulder, applejack wondered for a second if it was rainbow dash, but her attention was brought back to the boy who held her wrists above her head with one hand, and the silver butterfly knife against her neck.

The boy pushed back his hood and lowered the knife. He was fairly dark skinned, but untanned. He had jet black hair, it was as dark as the boys pupils. He had a cut that ran from his forehead, over his right eye, down his nose, across his lips, and ended at his chin.

"I'm going to take my hand off your mouth, do you promise not to scream." Applejacks attacker asked. Applejack nodded, worrie still in her eyes.

The boy took his hand off her mouth, "LET ME GO YA BASTURD, I'LL KICK YER ASS!" Applejack yelled. The boy quickly covered her mouth again.

The girl with the rainbow hair took off her hood. It WAS rainbow dash. "AJ, do what he says." Rainbow said calmly. "These guys or ok," she shot a targeting look at the boy holding applejack. "They're just bad at saying hello."

The boy in the back lowered his hood, his skin was very pale, a few scars an his face, but they were mostly healed. His hair was dirty blonde, he was older than the others, maybe twenty seven. "Let her go, we're trying to recruit her not kill her."

Applejack got her mouth free, "Recruit me? Fer what?" Applejack was confused. Her arms were released and the knife returned.

"Applejack come with us, there is something we need you for." Rainbow dash stepped up to her friend, "do it for me?"

"Fine, but this lunitic better not touch me again." Applejack snapped at the boy who grabbed her.

"AJ this is Blazing Star and Shadow Fire." Rainbow gestured towards the other two.

They walked to a building on the outskirts of town, where blazing star, the oldest, tapped a metal door and said, "code one-four-two." The door slid open and a middle aged man in a large coat, the same style as the three that brought applejack to the large building greeted them.

"New recruit?" Asked the man.

"Yep, a rank four. It's been a while since we've seen one so strong." Said shadow fire, the one who held applejack against the wall. For a guy who almost killed applejack, shadow was being pretty friendly to her. The three lead applejack to a large room deep within the building. They walked under a stone arch and into a massive, concrete, circular room. The ceiling must have been thirty meters high, and twenty meters from wall to wall. Applejack looked around in awe at the candle lit room.

"This is the corranation hall, in the morning, you will take the oath to be accepted should you choose to join us."

"Accepted? Accepted for what?"

"A place among the brotherhood."

Part 2: Reasoning

Rainbow dash was giving applejack a tour of the assassin headquarters. Dash's wings were folded up against her back, applejack almost stapled them there after rainbow kept brushing her face with them. Rainbow told her friend the tales of the assasins and templars, and the history of the order.

"We fight for peace, to protect those who cant protect themselves." Rainbow dash explained, "we fight for the good of people." Applejack ha never seen her best friend so serious. Dash explained the order and the creed, she went through the three tenets, and the three ironies.

"Hey dashy, do you really think this is the place for me? I mean i have a family, the farm. I have a life away from this place, i dont know if ah can just drop everythin and be an assassin,"

"We all had to make sacrifices for the brotherhood, but trust me, it's worth it."

They arrived a very long hallway, with doors on both sides, stretching farther than applejack could see. Rainbow dash brought her friend to room one hundred thirty seven. "There is good news and bad news about this room," rainbow paused, "the good news is that you and i are gona be roommates, the bad news is that we're gona be roommates." Dash finished. They both knew that living togeter could be fun, but they also knew that they hated how the other lived with a passion. Rainbow dash left things messy, on the floor, and wouldnt know the definition of the word clean if it hit her in the face. Applejack on the other hand was neat, thing were put in drawers, the room was organized, and just might jump out the window if she were forced to stay at rainbow dash's house for a week.

"Look, i still dont know, i support the cause, but i'm no killer, and even if ah was, i still have a life."

"I understand, just, if you change your mind, be back by morning. Just promise you will at least consider it."

"Ok dashy." And with that, applejack walked out of the large building and went back to her farm.

"Where were ya apples? You've been gone for almost two hours."

"Sorry mac, rainbow and i were at lunch." The large stallion just looked at his sister, sensing she was lying, but just waved the feeling off and sent her back to applebloom in the fields.

"While you were gone i pulled ahead, you're a good hundred fifty apples behind." Applebloom said with a laugh.

"Maybe, but i've come back from worse." The older sister said. The blonde picked up her machete and climbed the nearest tree. Applejack was working hard, an continued to work through dinner. She caught up to her sister while she was eating, and passed her as applebloom came back into the fields. They were neck and neck, but applebloom had just gotten to rest, while her sister was worn out.

"Last tree of the day!" Called out the younger sister a she ran to the last tree in the south field that still had apples to be picked.

"Oh no you dont." Said applejack as she sprinted for the same tree. Applebloom was at the trunk ad began climbing when applejack remembered something she saw an assassin practicing when they passed the training room. Applejack jumped up over her sister's head and stabbed the tree with her machete, using it like a branch to pull up on. She got to the top and cut all the apples out of the tree.

"Thirty five, thirty six, thirty seven. That's nine hundred thirty seven fer me, and nine hundred twenty fer you, looks like ah win lil sis." Applejack bragged. They went inside talking, joking, and laughing. Applejack scarfed down the dinner she missed several hours before, then walked upstairs to her bedroom. It had been a long day and applejack was tired. She flopped onto her bed like a flounder and fell asleep the second her head hit the pillow. It was about three in the morning when applejack heard noises coming from applebloom's room. Applejack rubbed her eyes and stumbled to the the door. She walked to her younger sister's room to investigate. The noises were getting louder, it sounded like a slowly opened the door as she flipped out her knife. Applejack was paralyzed to see a tall cloaked girl sliding a knife over appleblooms forehead.

"AAAGGHHH!" Applebloom screamed in agony. The cloaked girl's jacket bore the templar symbol that applejack had seen inscribed on the walls at the assassin HQ.

"Little applebloom," the templar was torturing the redhead. "So strong, so much willpower, but not enough. Hmhm." The templar teased with a devilish smile. "Now im going to ask you again," the cloaked woman ran the dull side of a long knife across applebloom's neck. "Where is your sister?"

'Why does she want me?' Applejack wondered for a second before snapping out of her trance. The templar had not seen applejack enter the room. The templar felt a tug on her shoulder, she turned around to see applejacks face.

"Dont you touch her ya bitch!" And with that, applejack planted her fist right on the templar's nose. Applejack pinned her sister's assailent against the wall and pressed the butterfly knife against her neck. "Who sent you?" Applejack asked, anger in her voice.

The templar was terrified, she had always made clean kills without her target knowing what happened, or a fight that she knew she would win, and even then her face was always covered. But this time, this time the target had the upperhand and was staring her straight in the eyes. "I- I- I cant say, ill be killed, im not even a full templar yet, this was just a training mission." She closed her eyes waiting for the end, but it never came, applejack wasnt going to murder her, not like this, not an exicution. Applejack used her knife to cut the templar cross off the girl's coat and held it up to her face.

"Ah aint heartless, so i aint gona kill ya now. But if ah ever see you again with this symbol, i will cut your throat faster than you can say 'templar'." Applejack punched the girl in the face, making her yelp. Then the blonde farmer walked the templar to the window and pushed her out onto the cold hard ground. It was a twenty foot drop but that wasnt really the first thing on applejack's mind. She walked to her little sister.

Applejack kneeled down to get a closer look at her sister's wounds. There was blood all over the redhead's face, bruises were also forming. Applebloom looked at her sister through watery eyes, "who was she? Why did she want you?"

"Ah dont know why she's after me, but i know she is a templar."

"A wha?"

"Look, it aint important now. You're hurt bad and ya need help." Applebloom was slipping in and out of conciousness, the blood loss had taken its toll on the girl. Applejack picked up her sister and wipped some blood off the redhead's face.

Applejack carried her little sister, though she was not so little anymore, and kicked open the hospital door. "HELP! ANYONE!" Applejack yelled. Three medics with a stretcher ran out to the girls. One of the doctors opened the stretcher as applejack placed her sister in the arms another doctor.

"What happened?" Asked the third medic.

"We, uhh-" applejack couldnt tell the truth, she may not have joined the assassins but she swore to never tell anybody about the order.

"Nevermind, you must be pretty stopped up after seeing her like this. What's her name?"

"Applebloom."

"Alright, we'll sort the rest out later." The medic walked into the door that the others had gone to. Applejack was held back when she tried to follow, so she sat in the waiting room. An hour, then two, then six went by. Applejack was very worried, but a man finally walked up to applejack.

"Is she ok?" Applejack coul barely talk.

"We don't know, she had several major injuries, possibly fatal. For now, all we can do is wait." Applejack was eventually let in to see her sister.

"Hey AJ." Applebloom coughed.

"Hey, how ya holdin up?" Applejack asked. She knew that the doctors hadn't told applebloom that she could be dead within several hours.

"Ah'm alright, dont't werrie 'bout me." Applejack wiped a tear off her sister's face. "You taught me ta be strong."

A nurse walked in and told applejack visiting hours had ended. "Ah love ya sis, just hold on, you'll be alright." Applejack left the room in tears, knowing that the next time applejack saw her sister, she could be in a casket.

Applejack walked through the streets, tears in her eyes, and hands in fists. She walked to the large concrete building where she had been taken earlier that day. Applejack hit the steele door with the bottom of her fist and said, "code one-four-two." The door slid open and applejack walked inside, ignoring the man who greeted her. She made her way to the corrination hall to find shadow fire and rainbow dash waiting. "How'd ya know i was comin back?"

"I heard what happened to applebloom."


	2. Chapter 2

Part 2: Reasoning

Rainbow dash was giving applejack a tour of the assassin headquarters. Dash's wings were folded up against her back, applejack almost stapled them there after rainbow kept brushing her face with them. Rainbow told her friend the tales of the assasins and templars, and the history of the order.

"We fight for peace, to protect those who cant protect themselves." Rainbow dash explained, "we fight for the good of people." Applejack ha never seen her best friend so serious. Dash explained the order and the creed, she went through the three tenets, and the three ironies.

"Hey dashy, do you really think this is the place for me? I mean i have a family, the farm. I have a life away from this place, i dont know if ah can just drop everythin and be an assassin,"

"We all had to make sacrifices for the brotherhood, but trust me, it's worth it."

They arrived a very long hallway, with doors on both sides, stretching farther than applejack could see. Rainbow dash brought her friend to room one hundred thirty seven. "There is good news and bad news about this room," rainbow paused, "the good news is that you and i are gona be roommates, the bad news is that we're gona be roommates." Dash finished. They both knew that living togeter could be fun, but they also knew that they hated how the other lived with a passion. Rainbow dash left things messy, on the floor, and wouldnt know the definition of the word clean if it hit her in the face. Applejack on the other hand was neat, thing were put in drawers, the room was organized, and just might jump out the window if she were forced to stay at rainbow dash's house for a week.

"Look, i still dont know, i support the cause, but i'm no killer, and even if ah was, i still have a life."

"I understand, just, if you change your mind, be back by morning. Just promise you will at least consider it."

"Ok dashy." And with that, applejack walked out of the large building and went back to her farm.

"Where were ya apples? You've been gone for almost two hours."

"Sorry mac, rainbow and i were at lunch." The large stallion just looked at his sister, sensing she was lying, but just waved the feeling off and sent her back to applebloom in the fields.

"While you were gone i pulled ahead, you're a good hundred fifty apples behind." Applebloom said with a laugh.

"Maybe, but i've come back from worse." The older sister said. The blonde picked up her machete and climbed the nearest tree. Applejack was working hard, an continued to work through dinner. She caught up to her sister while she was eating, and passed her as applebloom came back into the fields. They were neck and neck, but applebloom had just gotten to rest, while her sister was worn out.

"Last tree of the day!" Called out the younger sister a she ran to the last tree in the south field that still had apples to be picked.

"Oh no you dont." Said applejack as she sprinted for the same tree. Applebloom was at the trunk ad began climbing when applejack remembered something she saw an assassin practicing when they passed the training room. Applejack jumped up over her sister's head and stabbed the tree with her machete, using it like a branch to pull up on. She got to the top and cut all the apples out of the tree.

"Thirty five, thirty six, thirty seven. That's nine hundred thirty seven fer me, and nine hundred twenty fer you, looks like ah win lil sis." Applejack bragged. They went inside talking, joking, and laughing. Applejack scarfed down the dinner she missed several hours before, then walked upstairs to her bedroom. It had been a long day and applejack was tired. She flopped onto her bed like a flounder and fell asleep the second her head hit the pillow. It was about three in the morning when applejack heard noises coming from applebloom's room. Applejack rubbed her eyes and stumbled to the the door. She walked to her younger sister's room to investigate. The noises were getting louder, it sounded like a slowly opened the door as she flipped out her knife. Applejack was paralyzed to see a tall cloaked girl sliding a knife over appleblooms forehead.

"AAAGGHHH!" Applebloom screamed in agony. The cloaked girl's jacket bore the templar symbol that applejack had seen enscribed on the walls at the assassin's base, this girl had the red templar cross,

"Little applebloom," the templar was torturing the redhead. "So strong, so much willpower, but not enough. Hmhm." The templar teased with a devilish smile. "Now im going to ask you again," the cloaked woman ran the dull side of a long knife across applebloom's neck. "Where is your sister?"

'Why does she want me?' Applejack wondered for a second before snapping out of her trance. The templar had not seen applejack enter the room. The templar felt a tug on her shoulder, she turned around to see applejacks face.

"Dont you touch her ya bitch!" And with that, applejack planted her fist right on the templar's nose. Applejack pinned her sister's assailent against the wall and pressed the butterfly knife against her neck. "Who sent you?" Applejack asked, anger in her voice.

The templar was terrified, she had always made clean kills without her target knowing what happened, or a fight that she knew she would win, and even then her face was always covered. But this time, this time the target had the upperhand and was staring her straight in the eyes. "I- I- I cant say, ill be killed, im not even a full templar yet, this was just a training mission." She closed her eyes waiting for the end, but it never came, applejack wasnt going to murder her, not like this, not an exicution. Applejack used her knife to cut the templar cross off the girl's coat and held it up to her face.

"Ah aint heartless, so i aint gona kill ya now. But if ah ever see you again with this symbol, i will cut your throat faster than you can say 'templar'." Applejack punched the girl in the face, making her yelp. Then the blonde farmer walked the templar to the window and pushed her out onto the cold hard ground. It was a twenty foot drop but that wasnt really the first thing on applejack's mind. She walked to her little sister.

Applejack kneeled down to get a closer look at her sister's wounds. There was blood all over the redhead's face, bruises were also forming. Applebloom looked at her sister through watery eyes, "who was she? Why did she want you?"

"Ah dont know why she's after me, but i know she is a templar."

"A wha?"

"Look, it aint important now. You're hurt bad and ya need help." Applebloom was slipping in and out of conciousness, the blood loss had taken its toll on the girl. Applejack picked up her sister and wipped some blood off the redhead's face.

Applejack carried her little sister, though she was not so little anymore, and kicked open the hospital door. "HELP! ANYONE!" Applejack yelled. Three medics with a stretcher ran out to the girls. One of the doctors opened the stretcher as applejack placed her sister in the arms another doctor.

"What happened?" Asked the third medic.

"We, uhh-" applejack couldnt tell the truth, she may not have joined the assassins but she swore to never tell anybody about the order.

"Nevermind, you must be pretty stopped up after seeing her like this. What's her name?"

"Applebloom."

"Alright, we'll sort the rest out later." The medic walked into the door that the others had gone to. Applejack was held back when she tried to follow, so she sat in the waiting room. An hour, then two, then six went by. Applejack was very worried, but a man finally walked up to applejack.

"Is she ok?" Applejack could barely talk.

"We don't know, she had several major injuries, possibly fatal. For now, all we can do is wait." Applejack was eventually let in to see her sister.

"Hey AJ." Applebloom coughed.

"Hey, how ya holdin up?" Applejack asked. She knew that the doctors hadn't told applebloom that she could be dead within several hours.

"Ah'm alright, dont't werrie 'bout me." Applejack wiped a tear off her sister's face. "You taught me ta be strong."

A nurse walked in and told applejack visiting hours had ended. "Ah love ya sis, just hold on, you'll be alright." Applejack left the room in tears, knowing that the next time applejack saw her sister, she could be in a casket.

Applejack walked through the streets, tears in her eyes, and hands in fists. She walked to the large concrete building where she had been taken earlier that day. Applejack hit the steel door with the bottom of her fist and said, "code one-four-two." The door slid open and applejack walked inside, ignoring the man who greeted her. She made her way to the corrination hall to find shadow fire and rainbow dash waiting. "How'd ya know i was comin back?"

"I heard what happened to applebloom."


	3. Chapter 3

Chapter 3: one of us

Applejack woke up to rainbow's screaming over why her cloths were not on the floor. "ARE YOU EVEN LISTENING TO ME?!" Rainbow shouted.

"Look, ah'm tired, it was a long night, and ah'm worried about applebloom. Ah'll be sure to throw your crap on the floor later." Applejack didn't even make eye contact with her new roommate.

A wave of guilt crashed on top of the rainbow haired girl's shoulders. "You're right, sorry. Maybe we can put off your acceptance ceremony untill your sister gets out of the hospital."

"What if she doesn't?"

"She will. Remember when you were in the hospital after the barn fire?you stayed strong for applebloom, and i know she will come through for you."

"Ah escaped the fire with a few burns, she almost bled out in my arms before we got close to the hospital. She's in a heck of a lot werse condition than i was."

"She will be fine, i promise."

"Ok" they both got up and walked to the corrination hall. Rainbow walked in first and joined the other assassins that stood in two lines. They all had their hoods up, arms crossed over their chests, and hidden blades extended. Applejack walked inside. She walked between the assassins that were all facing towards her. When she got to the center of the room, applejack stopped in front of an old man with black assassin's robes and a long white beard.

"Applejack. You are about to be accepted into the most sacred order known to Equestria, but first you must swear to uphold the creed of the assassins. Do you swear to stay your blade from the innocent?"

"Ah swear."

"Do you swear to hide in plain sight, using those around you as your camouflage?"

"I swear."

"Do you swear to never compromise the brotherhood, revealing it nor any of its members to anyone outside of the order."

"I swear." The man put his hand on the newest assassin's shoulder. "Welcome to the brotherhood applejack." There was an applause, but applejack's focus was on rainbow dash, who was smiling right at back at her.


End file.
